In the season finale of the second season, most of the secrets of the Supercomputer and such were revealed. It turned out that Aelita was human and Hopper was her father, and he had created Lyoko and XANA to destroy Project Carthage, some sort of military operation years ahead of its time.

Four seasons of Code Lyoko have been broadcasted. The fourth season ended on France 3 in November 2007. On Cartoon Network it will be finished on some unknown date, although Cartoon Network is currently showing some of the last episodes on its website before they are broadcast.

The first season of the show has very little plot development. The only major plot developments are made in the two-part finale. The rest of the episodes are mostly filler. Until the finale, each episode consists of the group discovering an attack, stopping the attack, and resetting time to cover it up. Other sub-plots are included, such as their relationships with one another and other students and teachers at the school. Usually the interaction with their classmates and teachers early in each episode contributes to Xana's attack. Throughout these events, Jeremie works on a program to materialize Aelita in order to shut down the supercomputer safely. He eventually develops the program in the two-part finale, but Xana takes measures to keep Aelita linked to the supercomputer, preventing the group from shutting it down without killing her in the process.

The second season, in contrast to the first, is much more plot-focused, though a decent portion of the episodes are still filler. The animation is more realistic and detailed, and Jim and Sissi's personalities have changed significantly, though some traces of their old personalities exist in some form. Aelita lives on Earth in the second season. In the first episode of the second season, she enrolls at Kadic under the name of Aelita Stones. She poses as a cousin of Odd, using a forged birth certificate created by Jeremie. Jeremie's new super scan program also means that Aelita doesn't need to stay on Lyoko to check for Xana's activity. Aelita also begins having visions of a life she supposedly never lived, and a man named Franz Hopper is shown to have connections to Lyoko. Also adding to the group's troubles is a new student named William Dunbar, who has begun to take an interest in Yumi.

Each member of the group now has vehicles to quickly transport them in Lyoko: Odd gets a hover skateboard called an "Overboard," Ulrich gets a one-wheeled motorcycle called an "Overbike," and Yumi gets a hover scooter called an "Overwing." Aelita can ride any vehicle by herself if necessary, but usually rides with another person. A fifth sector, Carthage, is discovered in Lyoko and turns out to be Xana's home sector, from which all of his data can be accessed, so the group goes on several journeys into this sector to do so. At the same time, Xana begins sending the Scyphozoa after Aelita to steal her memories, and has created three other new monsters, as well. The operations of the supercomputer are also somewhat demystified. Return trips are fewer (though still common) now, because it makes Xana stronger. Eventually, Xana's true purpose is revealed, as are the origins of the supercomputer, Lyoko, and Aelita herself.

In the third season, Xana has been strangely quiet in both the real world and Lyoko, having done nothing during the group's summer vacation. It still needs a computer to exist, but is no longer limited to a specific one, instead being free to roam the internet at will. Jeremie has developed a new scanning program capable of tracking Xana, which reveals that Xana appears to be residing in the United States, but lacks the means to strike against Xana. Jeremie's current goal at the moment is to find a way to transfer the group into the internet.

Because Aelita had her memories returned by Franz Hopper, she can be devirtualized normally. She even has a new power to defend herself with in Lyoko shooting energy blasts from her hand's which she and Jeremie call,an Energy Field. Also, Yumi has decided against having a relationship with Ulrich, preferring to remain just friends.

In Carthage, the group finds Lyoko's core, which Xana wants destroyed. Being free of the supercomputer, Xana's attacks are far more powerful. Tower activation is still required to initiate them, but Xana can perform attacks on levels far beyond what he could when imprisoned. Xana can possess mass numbers of people at once, making it that much more difficult for the group to make their way from the school to the factory. In the hopes of isolating the group from Carthage, since destroying Lyoko directly would prove difficult, Xana has turned his sights to Lyoko's sectors, hoping to remove their ability to access Carthage by deleting the sectors they use to get there. By using the Scyphozoa to possess Aelita, Xana can use her to enter the code "Xana" in a passage tower. This gives Xana full access to the sector, after which he can delete it. Despite their best efforts, Xana eventually succeeds in deleting all four sectors. Luckily, Jeremie finds a way to access Carthage directly.

Seeing that their numbers aren't enough against Xana's increasing power, the group decides to add William Dunbar to the team to balance things out. This proves to be a disastrous mistake, however, as during William's first trip to Lyoko, Xana uses the Scyphozoa to possess him. Using William, Xana is easily able to overpower the other Lyoko warriors and destroy Lyoko's core. The act renders the supercomputer useless. Within the empty supercomputer, William transforms into a dark version of himself, now possessed by Xana to an even greater degree. Afterwards, Jeremie gets a coded message from the internet from none other than Franz Hopper, who somehow survived the destruction of Lyoko.

In the fourth season, Lyoko is recreated, allowing the group to continue tracking Xana. Traveling into the digital sea in Jeremie's latest creation, a submersible ship called the Skidbladnir, the group finds a number of "Replikas", which are single-sector recreations of Lyoko. Each of these Replikas is controlled by another supercomputer, which is in turn controlled by Xana. To stop Xana once and for all, Jeremie devises a way to materialize his friends at the site of these supercomputers with their Lyoko abilities intact, giving them the necessary firepower to dismantle them, all while continuing to battle the evil William. The group has new outfits and weapons to accompany the new season.

William is controlled by Xana, and acts as a barrier in Lyoko, the Digital Sea, and the Replikas. He is eventually freed, and in the second-to-last episode, Franz Hopper gives up his life to help in stopping Xana. Xana is defeated, and the group finally turns off the supercomputer.

The early theatrical trailer of the unreleased film was released by 20th Century Fox and Antefilms Pictures. In place of a fifth season, Moonscoop is planning to create three animated films at a length of 70 minutes each. It is unknown if they will ever go through with this idea.

There is a Book series of comic books currently beeing produced by Moonscoop that depict the adventures of Team Lyoko with screenshots of the episodes. The book series misspells the names of the characters often, like saying Jeremie is spelled Jeremy and Sissi, Sissy. They also misspelled the name of an episode; they said Teddygozilla was spelled Teddy-godzilla. They are all paperback.

Code Lyoko's status of being France's currently most popular animation internationally was given official recognition in December 2006, when it won France's prestigious Prix de l'Export 2006 Award for Animation.[1] The French fans gave the show their stamp of approval when they voted it no. 1 show on the Canal J website.